ggplot_onegeno: Plot one individual's genome-wide genotypes

In byandell/qtl2ggplot: Data Visualization for QTL Experiments

Plot one individual's genome-wide genotypes

Description

Plot one individual's genome-wide genotypes

Usage

ggplot_onegeno(
  geno,
  map,
  ind = 1,
  chr = NULL,
  col = NULL,
  shift = FALSE,
  chrwidth = 0.5,
  ...
)

Arguments

geno	Imputed phase-known genotypes, as a list of matrices (as produced by maxmarg) or a list of three-dimensional arrays (as produced by guess_phase).
map	Marker map (a list of vectors of marker positions).
ind	Individual to plot, either a numeric index or an ID (can be a vector).
chr	Selected chromosomes to plot; a vector of character strings.
col	Vector of colors for the different genotypes.
shift	If TRUE, shift the chromosomes so they all start at 0.
chrwidth	Total width of rectangles for each chromosome, as a fraction of the distance between them.
...	Additional graphics parameters

Value

object of class ggplot.

Examples

# load qtl2 package for data and genoprob calculation
library(qtl2)

# read data
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))

# insert pseudomarkers into map
map <- insert_pseudomarkers(iron$gmap, step=1)

# calculate genotype probabilities
probs <- calc_genoprob(iron, map, error_prob=0.002)

# inferred genotypes
geno <- maxmarg(probs)

# plot the inferred genotypes for the first individual
ggplot_onegeno(geno, map, shift = TRUE)

# plot the inferred genotypes for the first four individuals
ggplot_onegeno(geno, map, ind=1:4)

byandell/qtl2ggplot documentation built on March 18, 2024, 8:54 a.m.